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• No ht-seq in main Galaxy menu?
  Why is there no way in the main Galaxy menu to produce a raw counts matrix (not normalized and no...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...
• plotting multiple bigwigs in agregate plots
  What's the right tool to plot multiple bigwigs around a reference point like TSS? Can you help me...
• To merge several count data into one matrix.
  Hello all. I would like to merge or combine my count data into one matrix for using Degust prog...
• voom normalized count data matrix (Differential count 0.3.0)
  Hi, I have used voom from the "Differential count" package and it worked smoothly. I would like t...
• Can limma's voom take normalized counts as input?
  Hi,      I am currently analyzing some RNASeq data from TCGA - which is data that has been proce...
• Normalization of RNA-seq data
  Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on...
• Deeptools compute matrix
  I love Deeptools, and so glad that galaxy has moved them to the main server. It's awesome! I can...
• stringtie output from multiple samples into an FPKM matrix
  Hi all, Anyone have a good set of steps to take the stringtie transcript-level expression output...
• How to write tests for tools that access built-in data from the data tables
  I am writing a tool wrapper for a tool that allows as FASTA file input something from the data-ta...
• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• Parallelizing BAM calculations using Intervals specified in Text File
  Greetings Galaxy, I have been attempting to parallelize some tools which use BAM files as input....
• Homer getDiffExpression.pl edgeR
  To complement out cuffdiff analysis we thought to take a parallel route using Homer. to do so we...
• DE analysis of miRNA after mapping with miRDeep2 quantifier
  After small RNA sequencing I performed adapter, quality, and length trimming on fastq files. I th...
• Cuffdiff Changes
  Hi, I am wondering why Cuffdiff suddenly gives many more significant DE genes? I have used same ...
• deepTools2: compute matrix error
  I get this error when trying to use computeMatrix in the DeepTools2 suite: Fatal error: Exit...
• Use multiple inputs in same script
  Hi all, I have a batch of 170 samples (represented by 170 comma-separated files) and am attempti...